You can encrypt libraries… But, you mention SSH, so I’m not certain what you are trying to achieve.
As for incremental updates to a file like a PST file, a PST file is a database. In order for Seafile or any other program to do that for that matter, it would have to have the ability to access those databases and manipulate them according to the specifications of the developer, in this case, Microsoft, while observing laws involved with manipulating intellectual property. Not only would it require a significant amount of code, it would also most likely require Seafile to utilize only those tools that Microsoft allows them to use. On top of that, Seafile would then have to chop the data up somehow in to smaller chunks for syncing. It isn’t feasible.
Thunderbird, however, operates entirely differently. It splits email folders into individual folders and each email is stored in its own file. So, it should lend itself well to being synced with Seafile.
I ditched Outlook several years ago because of the “Everything in one massive file” issue, long before I ever used Seafile. It’s a huge risk storing massive amounts of critical data in one file, and it’s why many database programs no longer do it, but rather split the data into blocks and such, in the same way Seafile does with its database.